Covid-19 Tracker: The Delta fog

Good morning Mission and welcome to Virus Village, your (somewhat regular) Covid-19 data dump.

Local case numbers continue to fall as hospitalizations remain stable (though new admissions continue to rise), positivity rates remain high and the R Number estimates widely diverge.

Tracking covid these days requires what the British poet John Keats called “Negative Capability; that is, when man is capable of being in uncertainties, mysteries, doubts, without any irritable reaching after fact & reason … “

I’m feeling very irritable this morning.

Reaching after fact and reason, a recent Stanford Grand Rounds came up with a lot of uncertainties, mysteries and doubts.

After nearly 18 months since the first shutdown in San Francisco, and a dumpster’s worth of pre-print studies, the collective lack of knowledge about the virus and the disease it causes is stunning. Now with Delta, it’s worse than ever.

One major problem is that is the lack of data. Nationally and locally, official pubic health agencies, after four decades of degrading and defunding, have been plagued by antiquated or nonexistent systems for collecting, analyzing and reporting data. “Following the science” can be difficult under these conditions.

Add politics to this mess and the resulting chaos, especially on a global level, is predictable. For what it’s worth, check out the UK after it fully reopened in mid-July.

The good news is the vaccine appears to be working to prevent hospitalizations and deaths. But infections, transmissions, and Long Covid: who knows?

So enjoy the fog of negative capability, and scroll down for today’s covid numbers.

The Centers for Disease Control data used for the chart lags behind the data supplied from San Francisco Department of Public Health. As of August 15, DPH reports that more than 77 percent of all San Francisco residents have received one dose, and more than 71 percent are completely vaccinated. On August 15, the seven-day rolling average of shots per day to new recipients was 583. For information on where to get vaccinated in and around the Mission, visit our vaccination page.

Due to a DPH reporting glitch, we don’t have our usual hospitalization graph. The visualization above is a screenshot from the sf.gov website. On Aug. 12, DPH reports there were 111 hospitalizations, 73 in Acute Care, 38 in ICU. Although the number of hospitalizations is stable, according to the CDC, the number of new admissions is rising. For the seven days ending Aug. 13, there were 87 new admissions to SF hospitals, a 26.09 percent increase over the prior seven days. Again, relying on CDC data, for the week ending Aug. 13, covid patients accounted for 5.8 percent of hospital beds (up .59 percent) and 13.8 percent of ICU beds (up 3.04 percent).

The latest report from the federal Department of Health and Human Services shows Zuckerberg San Francisco General Hospital with 16 covid patients and 70 percent ICU occupancy, while across the Mission, CPMC had 15 covid patients and 70 percent ICU occupancy. Of 99 reported covid patients, 48 were at either SFGH or UCSF.

Between June 12 and Aug. 11, DPH reported 552 new cases among Mission residents (or 94 new cases per 10,000 residents) and 607 new cases in Bayview Hunters Point (160 new cases per 10,000 residents). Other than Bayview Hunters Point, six other neighborhoods had new case rates in excess of 100 per 10,000 residents, including the Castro, SOMA, Western Addition, Japantown, Hayes Valley and Bernal Heights. A case count map looks again like a Tale of Two Cities.

For the week ending Aug. 8, the seven-day rolling average of daily new cases in the city was 225 new cases, or approximately 25.1 new cases per day per 100,000 residents (based on 896,000 population).

August case numbers will not be available until Aug. 20. In July, White San Franciscans accounted for 35.1 percent of all new cases; Latinx, 21.2 percent; Asians, 15.7 percent; Blacks, 13.6 percent; multi-racial groups, 1.5 percent; Pacific Islanders, 1.1 percent,

Testing is rising again around the city, and positivity rates remain high. From June 12 through August 11, DPH reports 15,786 tests in the Mission for a rate of 269 tests per 1,000 residents. The positivity rate in the Mission during that time was 4.4 percent. Testing and positivity rates appear to be highest in the southeast sector. Bayview Hunters Point had a testing rate of 314 per 1,000 residents and a positivity rate of 6.4 percent, the city’s highest positivity rate

DPH reports 2 new covid-related deaths in August, but July totals remained at 9. Nonetheless, covid-related deaths, according to DPH, now stand at 570 (an increase of three over recent days). Though not specified, it appears from other data (see below) that the two August deaths were nursing home residents.

Covid R estimation has raised its San Francisco R Number estimate to a 1.09, one of the better numbers in California, where it estimates the R Number at 1.24, indicative of substantial prevalence and spread around the state. Models in the ensemble are split with an average estimate; the San Francisco R Number is still below 1, but rising to .91 and the California R Number at 1.08.

DPH no longer provides numbers on unhoused residents. As of Aug. 11, in nursing homes (“Skilled Nursing Facilities”), there were six new cases and two new Covid-related deaths. Single Resident Occupancy hotels (SROs) reported 53 new cases and 0 new deaths.